tbuckley/cabot-search huggingface dataset:
Application of non-invasive methods of assessment of steatosis and fibrosis in chronic diffuse liver diseases of various etiologies
Authors: Yu.M. Stepanov, V.I. Didenko, O.P. Petishko, A.M. Galinska
Journal: GASTROENTEROLOGY (2023)

Background. The aim of the study is to analyze the parameters of liver steatosis and fibrosis based on shear wave elastography (SWE) and steatometry data in patients with chronic diffuse liver diseases, taking into account the etiological factor, and determine the diagnostic accuracy of SWE in the diagnosis of liver fibrosis. ­Materials and methods. Three hundred and sixty-four patients with chronic diffuse liver disease aged (48.00 ± 1.84) years were examined, 159 (43.7 %) were male, and 205 (56.3 %) female. The patients were divided into groups: 108 people with non-alcoholic fatty liver disease (NAFLD), 143 with chronic hepatitis C (HCV), 56 with alcoholic liver disease (ALD), and 57 with drug-induced toxic hepatitis. In all patients, SWE and steatometry were performed by Soneus P7 device (Kharkiv, Ukraine) with the liver stiffness and ultrasound attenuation coefficient measurement. Results. According to SWE data, 270 (74.2 %) patients with chronic liver disease had fibrotic changes in the liver. A significant increase in liver stiffness by 1.9 times (p &lt; 0.05) according to Young’s modulus was found in HCV patients and by 1.4 times (p &lt; 0.05) in ALD patients compared to the control group, by 1.7 (p &lt; 0.05) and 1.3 times (p &lt; 0.05), respectively, compared to the group of patients with NAFLD. According to steatometry data, an increase in ultrasound attenuation coefficient by 30.2 % (p &lt; 0.05) in patients with NAFLD, by 27.5 % (p &lt; 0.05) in those with ALD and by 22 % (p &lt; 0.05) in people with toxic hepatitis was found compared to the control group. In patients with liver fibrosis, the median liver stiffness was 6.70 kPa (6.35, 7.56), while in those without liver fibrosis, this parameter was 1.2 times lower (p &lt; 0.01). Histological evaluation of liver samples obtained through percutaneous biopsy in 75 patients with chronic liver disease demonstrated the absence of fibrosis in 14 (18.7 %) cases. According to the results of the ROC analysis, the cut-off value of the liver stiffness determined by SWE was 5.79 kPa, confirming the presence of liver fibrosis in patients with chronic liver disease regardless of etiology (AUC = 0.901, p &lt; 0.001). Conclusions. The liver stiffness determined by SWE in HCV and ALD patients was higher than in NAFLD patients (p &lt; 0.05), as well as the frequency of F3–4 stages of liver fibrosis (p &lt; 0.05). The threshold value of the liver stiffness for liver fibrosis diagnosis in chronic liver disease regardless of etiology was 5.79 kPa (sensitivity 100.0 %, specificity 85.7 %), which allows the family doctor to form a risk group of patients who needed dynamic monitoring with a further investigation of the etiological factor of liver fibrosis.
Highlight: Genetic Signatures of Chickpea's Cultural Crossroads
Authors: Casey McGrath
Journal: Molecular Biology and Evolution (2023)

A map derived from Nikolai Vavilov's original depiction of chickpea domestication centers (Roman numerals) showing chickpea dispersal routes (arrows) from its center of domestication in Southwest Asia to South and Central Asia and East Africa.Inset shows the desi and kabuli market classes of chickpea.
Travel-Related Diagnoses Among U.S. Nonmigrant Travelers or Migrants Presenting to U.S. GeoSentinel Sites — GeoSentinel Network, 2012–2021
Authors: Ashley B. Brown, Charles Miller, Davidson H. Hamer, Phyllis Kozarsky, Michael Libman, Ralph Huits, Aisha Rizwan, Hannah Emetulu, Jesse Waggoner, Lin H. Chen, Daniel T. Leung, Daniel Bourque, Bradley A. Connor, Carmelo Licitra, Kristina M. Angelo
Journal: MMWR Surveillance Summaries (2023)

During 2012-2021, the volume of international travel reached record highs and lows. This period also was marked by the emergence or large outbreaks of multiple infectious diseases (e.g., Zika virus, yellow fever, and COVID-19). Over time, the growing ease and increased frequency of travel has resulted in the unprecedented global spread of infectious diseases. Detecting infectious diseases and other diagnoses among travelers can serve as sentinel surveillance for new or emerging pathogens and provide information to improve case identification, clinical management, and public health prevention and response.
<i>Notes from the Field</i>: Emergence of an Mpox Cluster Primarily Affecting Persons Previously Vaccinated Against Mpox — Chicago, Illinois, March 18–June 12, 2023
Authors: Emily A. G. Faherty, Taylor Holly, Yasmin P. Ogale, Gordon Crisler, Ashley Becht, David Kern, Lavinia Nicolae, Hillary Spencer, Michael Wasz, Janna L. Kerins, Alyse Kittner, Amber Staton, Carla Hardnett, Christina Hutson, Crystal M. Gigante, Laura Quilter, Ian Kracalik, Stephanie Black, Andrea M. McCollum, Agam K. Rao, Irina Tabidze
Journal: MMWR Morbidity and Mortality Weekly Report (2023)
Small RNA modifications: regulatory molecules and potential applications
Authors: Qunli Xiong, Yaguang Zhang
Journal: Journal of Hematology & Oncology (2023)

Abstract Small RNAs (also referred to as small noncoding RNAs, sncRNA) are defined as polymeric ribonucleic acid molecules that are less than 200 nucleotides in length and serve a variety of essential functions within cells. Small RNA species include microRNA (miRNA), PIWI-interacting RNA (piRNA), small interfering RNA (siRNA), tRNA-derived small RNA (tsRNA), etc. Current evidence suggest that small RNAs can also have diverse modifications to their nucleotide composition that affect their stability as well as their capacity for nuclear export, and these modifications are relevant to their capacity to drive molecular signaling processes relevant to biogenesis, cell proliferation and differentiation. In this review, we highlight the molecular characteristics and cellular functions of small RNA and their modifications, as well as current techniques for their reliable detection. We also discuss how small RNA modifications may be relevant to the clinical applications for the diagnosis and treatment of human health conditions such as cancer.
Progress Toward Rubella Elimination — World Health Organization South-East Asia Region, 2013–2021
Authors: Sudhir Khanal, Sunil Bahl, Lucky Sangal, Deepak Dhongde, Patrick Michael O’Connor, Natasha S. Crowcroft, Michelle Morales
Journal: MMWR Morbidity and Mortality Weekly Report (2023)

During 2013, the 11 countries of the World Health Organization (WHO) South-East Asia Region* (SEAR) adopted the goals of measles elimination and rubella and congenital rubella syndrome (CRS) control† by 2020. During 2019, SEAR countries declared a broader goal for eliminating both measles and rubella§ by 2023 (1). Before 2013, only five SEAR countries had introduced rubella-containing vaccine (RCV). This report updates a previous report and describes progress toward rubella elimination in SEAR during 2013-2021 (2). During 2013-2021, six SEAR countries introduced RCV; all countries in the Region now use RCV in routine immunization. Routine immunization coverage with the first dose of a rubella-containing vaccine (RCV1) increased >600%, from 12% during 2013 to 86% during 2021, and an estimated 515 million persons were vaccinated via RCV supplementary immunization activities (SIAs)¶ during 2013-2021. During this time, annual reported rubella incidence declined by 80%, from 5.5 to 1.1 cases per million population. Maldives and Sri Lanka are verified as having achieved rubella elimination; Bhutan, North Korea, and Timor-Leste have halted endemic transmission of rubella virus for >36 months. SEAR has made substantial progress toward rubella elimination; however, intensified measures are needed to achieve elimination.
An ATP-sensitive phosphoketolase regulates carbon fixation in cyanobacteria
Authors: Kuan-Jen Lu, Chiung-Wen Chang, Chun-Hsiung Wang, Frederic Y-H Chen, Irene Y. Huang, Pin-Hsuan Huang, Cheng-Han Yang, Hsiang-Yi Wu, Wen-Jin Wu, Kai-Cheng Hsu, Meng-Chiao Ho, Ming-Daw Tsai, James C. Liao
Journal: Nature Metabolism (2023)

Abstract Regulation of CO 2 fixation in cyanobacteria is important both for the organism and global carbon balance. Here we show that phosphoketolase in Synechococcus elongatus PCC7942 ( Se XPK) possesses a distinct ATP-sensing mechanism, where a drop in ATP level allows Se XPK to divert precursors of the RuBisCO substrate away from the Calvin–Benson–Bassham cycle. Deleting the Se XPK gene increased CO 2 fixation particularly during light–dark transitions. In high-density cultures, the Δxpk strain showed a 60% increase in carbon fixation and unexpectedly resulted in sucrose secretion without any pathway engineering. Using cryo-EM analysis, we discovered that these functions were enabled by a unique allosteric regulatory site involving two subunits jointly binding two ATP, which constantly suppresses the activity of Se XPK until the ATP level drops. This magnesium-independent ATP allosteric site is present in many species across all three domains of life, where it may also play important regulatory functions.
A neural mechanism for terminating decisions
Authors: Gabriel M. Stine, Eric M. Trautmann, Danique Jeurissen, Michael N. Shadlen
Journal: Neuron (2023)

The brain makes decisions by accumulating evidence until there is enough to stop and choose. Neural mechanisms of evidence accumulation are established in association cortex, but the site and mechanism of termination are unknown. Here, we show that the superior colliculus (SC) plays a causal role in terminating decisions, and we provide evidence for a mechanism by which this occurs. We recorded simultaneously from neurons in the lateral intraparietal area (LIP) and SC while monkeys made perceptual decisions. Despite similar trial-averaged activity, we found distinct single-trial dynamics in the two areas: LIP displayed drift-diffusion dynamics and SC displayed bursting dynamics. We hypothesized that the bursts manifest a threshold mechanism applied to signals represented in LIP to terminate the decision. Consistent with this hypothesis, SC inactivation produced behavioral effects diagnostic of an impaired threshold sensor and prolonged the buildup of activity in LIP. The results reveal the transformation from deliberation to commitment.
Higher alcohol consumption was associated with greater incidence of total hip replacement due to hip osteoarthritis in a dose‐dependent manner in women: comment on the article by Marchand et al
Authors: Gang Wang, Zhichun Liu, Ning Zhuo
Journal: Arthritis & Rheumatology (2023)

Disclosure Form Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Genomic approaches to cancer and minimal residual disease detection using circulating tumor DNA
Authors: Nicholas P Semenkovich, Jeffrey J Szymanski, Noah Earland, Pradeep S Chauhan, Bruna Pellini, Aadel A Chaudhuri
Journal: Journal for ImmunoTherapy of Cancer (2023)

Liquid biopsies using cell-free circulating tumor DNA (ctDNA) are being used frequently in both research and clinical settings. ctDNA can be used to identify actionable mutations to personalize systemic therapy, detect post-treatment minimal residual disease (MRD), and predict responses to immunotherapy. ctDNA can also be isolated from a range of different biofluids, with the possibility of detecting locoregional MRD with increased sensitivity if sampling more proximally than blood plasma. However, ctDNA detection remains challenging in early-stage and post-treatment MRD settings where ctDNA levels are minuscule giving a high risk for false negative results, which is balanced with the risk of false positive results from clonal hematopoiesis. To address these challenges, researchers have developed ever-more elegant approaches to lower the limit of detection (LOD) of ctDNA assays toward the part-per-million range and boost assay sensitivity and specificity by reducing sources of low-level technical and biological noise, and by harnessing specific genomic and epigenomic features of ctDNA. In this review, we highlight a range of modern assays for ctDNA analysis, including advancements made to improve the signal-to-noise ratio. We further highlight the challenge of detecting ultra-rare tumor-associated variants, overcoming which will improve the sensitivity of post-treatment MRD detection and open a new frontier of personalized adjuvant treatment decision-making.
Avoiding <scp>implant‐related</scp> complications in medically compromised patients with or without unhealthy lifestyle/Elevated oxidative stress
Authors: Gregorio Guabello, Francesco Zuffetti, Andrea Ravidà, Matteo Deflorian, Giorgio Carta, Muhammad H. A. Saleh, Matteo Serroni, Bernhard Pommer, Georg Watzek, Luca Francetti, Tiziano Testori
Journal: Periodontology 2000 (2023)

Abstract Increased human life expectancy broadens the alternatives for missing teeth and played a role in the widespread use of dental implants and related augmentation procedures for the aging population. Though, many of these patients may have one or more diseases. These systemic conditions may directly lead to surgical complications, compromise implant/bone healing, or influence long‐term peri‐implant health and its response to biologic nuisances. Offering patients credible expectations regarding intra‐ and postoperative complications and therapeutic prognosis is an ethical and legal obligation. Clear identification of potential types of adverse effects, complications, or errors is important for decision‐making processes as they may be related to different local, systemic, and technical aspects. Therefore, the present review structures the underlying biological mechanisms, clinical evidence, and clinical recommendations for the most common systemic risk factors for implant‐related complications.
A National Study Exploring the Association Between Fluoride Levels and Dental Fluorosis
Authors: Man Hung, Eric S. Hon, Amir Mohajeri, Hyma Moparthi, Teresa Vu, Jason Jeon, Martin S. Lipsky
Journal: JAMA Network Open (2023)

Importance While the effects of fluoride on health have been widely researched, fewer high-quality studies examine the association of fluoride levels in water and dental fluorosis. Objective To investigate the association between fluoride exposure from drinking water and dental fluorosis. Design, Setting, and Participants This cross-sectional study used the 2013-2014 and 2015-2016 National Health and Nutrition Examination Survey (NHANES) data (January 1, 2013, through December 31, 2016). NHANES uses a complex sampling technique to develop nationally representative sample estimates of the US population that consists of interviews and physical assessments. Children and adolescents aged 6 to 15 years were included because NHANES contains their data for all 3 forms of fluoride measures: plasma fluoride levels, water levels of fluoride, and dietary fluoride supplementation. Data were analyzed from January 1 to April 30, 2023. Exposures Water and plasma fluoride levels were measured by laboratory personnel. Dietary fluoride supplement data were self-reported. Main Outcomes and Measures The Dean’s Fluorosis Index was used to evaluate fluorosis status for each tooth. The dental fluorosis severity value was based on the second most affected tooth. Independent variables included plasma and water fluoride concentrations and dietary fluoride supplementation. An independent samples t test was used to compare fluoride exposures between groups, and Pearson correlation assessed the association between plasma and water fluoride levels. To assess whether fluoride exposures were associated with dental fluorosis, logistic regression analyses were conducted. Results There were 1543 participants in the 2013-2014 NHANES cycle (weighted proportion male, 51.9%; mean [SD] age, 11.0 [2.7] years) and 1452 in the 2015-2016 cycle (weighted proportion male, 52.6%; mean [SD] age, 11.1 [2.8] years). A weighted 87.3% exhibited some degree of fluorosis in the 2013-2014 cycle and 68.2% in the 2015-2016 cycle. After adjusting for covariates in the 2015-2016 cycle, both higher water and plasma fluoride concentrations were associated with higher odds of dental fluorosis: adjusted odds ratios [AORs], 2.378 (95% CI, 1.218-5.345]) for water fluoride and 1.568 (95% CI, 1.038-2.499) for plasma fluoride. Fluoride supplements were not significantly associated with dental fluorosis: AOR, 0.741 (95% CI, 0.367-1.408). Conclusions and Relevance The findings of this cross-sectional study suggest that exposure to higher concentrations of fluoride in water and having higher plasma levels of fluoride were associated with a greater risk of dental fluorosis. Further research can help policy makers develop policies that balance substantial caries prevention with the risk of dental fluorosis.
Characteristics of Medical Evacuation by Train in Ukraine, 2022
Authors: Stig Walravens, Albina Zharkova, Anja De Weggheleire, Marie Burton, Jean-Clément Cabrol, James S. Lee
Journal: JAMA Network Open (2023)

Importance The 2022 war in Ukraine severely affected access to health care for patients in the conflict-affected regions and limited options for medical evacuation. Air transport, a common method of medical evacuation in war zones, was unsafe due to the conflict of 2 modernized military forces that were in possession of aircraft and surface-to-air weapons; therefore, Médecins Sans Frontières, in collaboration with the Ukrainian railway company and Ukrainian health agencies, addressed this by initiating medical evacuation via medically customized trains. Objective To describe the implementation of medical evacuation trains aimed at improving the access to health care for war-affected patients. Design, Setting, and Participants This case series describes the remodeling of 2 trains used for medical evacuation in a conflict zone during the war in Ukraine. The study was conducted from March 30 to November 30, 2022. One train had minimal adjustments and could be rapidly deployed to address the most pressing humanitarian needs, while the other underwent major structural modifications to provide intensive care capacity. The report details the medical capabilities of the trains, the organization of referrals, and operational challenges encountered. Additionally, it includes a case series on the characteristics of patients transported in the initial 8 months, based on routinely collected programmatic descriptive data of all patients transported by the medical trains. Results In 8 months, 2481 patients (male-female ratio, 1.07; male, 1136 [46%]; female 1058 [43%]; missing data, 287 [12%]; median age, 63 years [range, 0-98 years]) were evacuated from 11 cities near the Ukrainian conflict frontline to safer areas. Initially, the trains predominantly evacuated trauma patients, but over the course of the war, the patient characteristics changed with more medical and nonacute conditions, and fewer trauma patients. The main reason for entry into the intensive care unit train carriage was for close monitoring and observation, and the main interventions performed were primarily for respiratory failure. Conclusions and Relevance The findings of this study suggest that medical evacuation in a war zone by converted trains is possible and can improve access to health care for war-affected patients. The presence of intensive care capacity on board allows for transport of more severely ill or injured individuals. However, the target population should not be limited to trauma patients, as health care institutions affected host a much broader population whose needs and urgency for evacuation may change over time.
Association of Size Matching Using Predicted Heart Mass With Mortality in Heart Transplant Recipients With Obesity or High Pulmonary Vascular Resistance
Authors: Ran Tao, Timothy M. Hess, Adam Kuchnia, Joshua Hermsen, Farhan Raza, Ravi Dhingra
Journal: JAMA Network Open (2023)

Importance Pretransplant obesity and higher pulmonary vascular resistance (PVR) are risk factors for death after heart transplant. However, it remains unclear whether appropriate donor-to-recipient size matching using predicted heart mass (PHM) is associated with lower risk. Objective To investigate the association of size matching using PHM with risk of death posttransplant among patients with obesity and/or higher PVR. Design, Setting, and Participants All adult patients (&amp;amp;gt;18 years) who underwent heart transplant between 2003 and 2022 with available information using the United Network for Organ Sharing cohort database. Multivariable Cox models and multivariable-adjusted spline curves were used to examine the risk of death posttransplant with PHM matching. Data were analyzed from October 2022 to March 2023. Exposure Recipient’s body mass index (BMI) in categories (&amp;amp;lt;18.0 [underweight], 18.1-24.9 [normal weight, reference], 25.0-29.9 [overweight], 30.0-34.9 [obese 1], 35-39.9 [obese 2], and ≥40.0 [obese 3]) and recipient’s pretransplant PVR in categories of less than 4 (29 061 participants), 4 to 6 (2842 participants), and more than 6 Wood units (968 participants); and less than 3 (24 950 participants), 3 to 5 (6115 participants), and 5 or more (1806 participants) Wood units. Main Outcome All-cause death posttransplant on follow-up. Results The mean (SD) age of the cohort of 37 712 was 52.8 (12.8) years, 27 976 (74%) were male, 25 342 were non-Hispanic White (68.0%), 7664 were Black (20.4%), and 3139 were Hispanic or Latino (8.5%). A total of 12 413 recipients (32.9%) had a normal BMI, 13 849 (36.7%) had overweight, and 10 814 (28.7%) had obesity. On follow-up (median [IQR] 5.05 [0-19.4] years), 12 785 recipients (3046 female) died. For patients with normal weight, overweight, or obese 2, receiving a PHM-undermatched heart was associated with an increased risk of death (normal weight hazard ratio [HR], 1.20; 95% CI, 1.07-1.34; overweight HR, 1.12; 95% CI, 1.02-1.23; and obese 2 HR, 1.07; 95% CI, 1.01-1.14). Moreover, patients with higher pretransplant PVR who received an undermatched heart had a higher risk of death posttransplant in multivariable-adjusted spline curves in graded fashion until appropriately matched. In contrast, risk of death among patients receiving a PHM-overmatched heart did not differ from the appropriately matched group, including in recipients with an elevated pretransplant PVR. Conclusion and Relevance In this cohort study, undermatching donor-to-recipient size according to PHM was associated with higher posttransplant mortality, specifically in patients with normal weight, overweight, or class II obesity and in patients with elevated pretransplant PVR. Overmatching donor-to-recipient size was not associated with posttransplant survival.
Ambulance Trains—From the Crimean War to Ukraine
Authors: Sanders Marble, Justin Barr
Journal: JAMA Network Open (2023)

Stig Walravens, MD; Albina Zharkova, MD, PhD; Anja De Weggheleire, MD, MPH; Marie Burton, MPH; Jean-Clément Cabrol, MD; James S. Lee, MD, MSc